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Supporting Info-Revised-2 1 SUPPORTING INFORMATION (SI) TAXON SAMPLING: Hynobiidae: The family includes 54 species in ten genera (AmphibiaWeb, 2012). Besides the type genus Hynobius, Onychodactylus is included in our data matrix as a basal taxon of the family (e.g., Zhang et al., 2006). The fossil record of Hynobiidae is extremely poor, with only fragmentary material known from the upper Pliocene of Kazakhstan (Averianov and Tjudkova, 1995), and from the upper Miocene and lower Pleistocene of Romania (Venczel, 1999). More recently, the Early Cretaceous Liaoxitriton from China has been recognized as a stem-group taxon of the family (Chen and Gao, 2009). Cryptobranchidae: The family consists of three species in two genera (AmphibiaWeb, 2012). We included both Cryptobranchus and Andrias in our data matrix. In addition, the Middle Jurassic fossil taxon Chunerpeton (Gao and Shubin, 2003) from China is also included in this study. The latter taxon was named and described based on well-preserved specimens from the Daohugou site near Ningcheng, Inner Mongolia. The fossil beds exposed at the Daohugou site were mistakenly correlated with the Early Cretaceous Yixian Formation (Wang et al., 2000), but have been consistently dated as 164-165 Ma by independent research groups (Chen et al., 2004; Liu et al., 2006; Yang and Li, 2008), and thus are Middle Jurassic (Bathonian-Callovian) in age. Dicamptodontidae and Rhyacotritonidae: The family Dicamptodontidae, commonly known as Pacific giant salamanders, includes four living species in the single genus Dicamptodon (AmphibiaWeb, 2012). In addition, Dicamptodon is recorded by fossil material from the Paleocene of Alberta, Canada (Naylor and Fox, 1993). Several other fossil taxa (Bargmannia from the Miocene of Slovakia, Chrysotriton from the lower Eocene of North Dakota, Geyeriella and Wolterstorffiella from the upper Paleocene of Germany) were previously assigned to the Dicamptodontidae solely based on the position of spinal nerve foramina (Estes, 1981; Roček, 1994), but these are currently treated as enigmatic forms with uncertain taxonomic positions (Milner, 2000; Venczel, 2008). Among these, the generic name Bargmannia Herre, 1955 has been found to be a junior homonym of the siphonophore Bargmannia Totton, 1954 (Naish, 2008). In any case, these problematic fossil taxa are not included in our phylogenetic analysis because of their uncertain taxonomic status (see Milner, 2000 for discussion). The monotypic family Rhyacotritonidae has four living species in the genus Rhyacotriton (AmphibiaWeb, 2012). Known as the torrent salamanders of the Pacific northwest region of the United States, Rhyacotriton was previously classified in Dicamptodontidae or Ambystomatidae, but has been formally recognized as the type genus of the Rhyacotritonidae by Good and Wake (1992). No fossils referable to the Rhyacotritonidae are known. Salamandridae: The family Salamandridae was traditionally subdivided into the “true salamanders” and the “newts,” but these informal groups have been formally recognized as the subfamilies Salamandrinae and Pleurodelinae, respectively (Dubois and Raffaëlli, 2009) based on the molecular analysis of Zhang et al. (2008). In addition, a third subfamily (Salamandrininae) has also been recognized to include Salamandrina and the Oligocene fossil genus Archaeotriton (Dubois and Raffaëlli, 2009). Our data matrix included three taxa of the family group: Taricha and Tylototriton as representatives of the Pleurodelinae, and Salamandra as the representative of 2 the Salamandrinae. Taricha has a fossil record extending to the Oligocene in North America, and both Salamandra and Tylototriton have been recorded from the Eocene of Europe (Estes, 1981; Venczel, 2008). Amphiumidae: The family includes the genus Amphiuma, with three living species and a Paleocene occurrence of the genus. All taxa are North American in distribution (Estes, 1981). The earliest record of the family is documented by Proamphiuma from the latest Cretaceous (see Gardner, 2003b). The fossil taxon Paleoamphiuma from the Eocene Green River Formation was reported as an amphiumid in the original publication (Rieppel and Grande, 1998), but a recent review of the fossil material has shown it may be a sirenid (Gardner, 2003b). Since a formal revision of the taxon is in progress, this significant taxon is excluded from our analysis until the correct information concerning it is available in publication. Nonetheless, inclusion or exclusion of this fossil taxon has no effect on the stratigraphic range of the family Amphiumidae or Sirenidae, as both families have an early record back to Cretaceous time (Estes, 1981; Milner, 2000; Gardner, 2003a, b). Proteidae: This is a small family including only the genera Necturus and Proteus. The former genus has five living species in North America, and the latter a single species known from Europe (AmphibiaWeb, 2012). Both genera are included in our data matrix. Necturus has a fossil record extending to the Paleocene in North America (Naylor, 1978a), and Proteus to the Pleistocene in Europe (Estes, 1981). In addition, fragmentary fossil material has been described under the names Mioproteus and Orthophyia from the Miocene of North Caucasus, Germany, and Hungary (Estes and Darevsky, 1977; Estes and Schleich, 1994; Roček, 2005), and from the Pliocene of Poland (Młynarski et al., 1984). These Neogene fossil proteids are not included in our phylogenetic analysis because both taxa are poorly diagnosed, being based on fragmentary material. Sirenidae: Another small family, consisting of Siren and Pseudobranchus, each with two species (AmphibiaWeb, 2012). The fossil record of the family is poor, with Habrosaurus as the only well-known genus, based on material from the Late Cretaceous (middle Campanian) and middle Paleocene of North America (Gardner, 2003a). Two Gondwanan fossil salamanders, Kababisha (Cenomanian, Sudan) and Noterpeton (Maastrichtian, Bolivia), each based on fragmentary material, were regarded as possible sirenids (Evans and Werner, 1996), but a recent review of the evidence has excluded these enigmatic taxa from the Sirenidae (Gardner, 2003a). Plethodontidae: Commonly known as “lungless salamanders,” the Plethodontidae are by far the most species diverse group of salamanders, having 419 species recognized at present (AmphibiaWeb, 2012). The family consists of two subfamilies, Hemidactyliinae and Plethodontinae. Two taxa are included in our data matrix, Plethodon and Desmognathus, both from the subfamily Plethodontinae. Ambystomatidae: The family includes a single genus Ambystoma, with 32 extant species named and described so far (AmphibiaWeb, 2012). Among these, Ambystoma mexicanum is probably the best-known salamander taxon with over thousand publications on various aspects of the famous salamander species. The earliest fossil record of the family is described under the name Ambystoma tiheni based on fossils from the lower Oligocene of Saskatchewan in western Canada 3 (Holman, 1968; Estes, 1981). Although classified in the Ambystomatidae, the ichnogenus Ambystomichnus Peabody, 1954 is known by trackways from Paleocene beds in Montana (Gilmore, 1928; Peabody, 1954) and Eocene beds of Wyoming (Foster, 2001). Because no character in our data matrix can be scored for Ambystomichnus, the ichnotaxon is excluded from our phylogenetic analysis. Mesozoic Fossil Taxa: In the past decade, a number of crown-group salamanders have been named and described based on the material from Jurassic and Cretaceous deposits in China. Several of these taxa are included in our data matrix: Chunerpeton, Pangerpeton, Liaoxitriton, and the new taxon Beiyanerpeton. Several other taxa (e.g., Laccotriton, Sinerpeton, and Jeholotriton) are excluded from this analysis because they are anatomically uncertain and are currently under taxonomic revision. Among Mesozoic salamanders known from North America, Iridotriton was described as a putative salamandroid based on a partial skeleton from the Upper Jurassic Morrison Formation (Evans et al., 2009). The Morrison Formation has yielded 40Ar/39Ar dates of 148-150 Ma (Kowallis et al., 1998), and thus, is Tithonian in age (International Commission on Stratigraphy, 2009). This Jurassic taxon (78% missing data in our data matrix) is included in our phylogenetic analysis because of its age, biogeographic significance, and its putative salamandroid affinity as described in the original publication. Among the Mesozoic salamanders known from Europe, Valdotriton from the Lower Cretaceous (Barremian) of Spain represents an important record (Evans and Milner, 1996), and this taxon is included in our analysis as a fossil representative of the Salamandroidea. Among the several salamanders known from the Kirtlington Quarry (Evans and Milner, 1994), Marmorerpeton and the undescribed “salamander A” are non-crown group salamanders (Evans and Milner, 1996; Milner, 2000). Also from the Kirtlington Quarry, the so-called “salamander B” is mentioned as a possible “crown-salamander” (Milner, 2000), but cannot be incorporated into a phylogenetic analysis before its nomenclatural status is established by formal publication with illustration and description of the specimens. CHARACTER CODING: The characters used in the phylogenetic analysis include both binary and multistate alternatives (e.g., Siddall and Jensen, 2003). Coding of skeletal characters for extant salamanders is based on information from representative specimens of each group and data published in the literature, with the sources of information as listed below.
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